This week – 19th-23rd October 2009 – is the Open Access week around the world – fitting nicely with the 5th birthday of PLoS Medicine. And when I say ‘around the world’ I really mean it. Just check out all the global events happening this week.

Many countries are participating this year, including some with numerous events all around the country. See, for example, all the events in Germany (there are 67 events in that country alone!), Netherlands, China and Japan.

As the week unfolds, we will blog more about it here. In the meantime, you can follow the news of the OA week on Facebook or by following PLoS on Twitter.You may also want to sign up to participate in the OASPA webinar (locationless – sign up to participate online).

Professor Seyed Ehtesham Hasnain is the Vice-Chancellor at the University of Hyderabad in India, and one of the most prolific authors in PLoS ONE. Last week, I interviewed Dr. Hasnain over e-mail about his work and his experience with PLoS ONE:

1. What is your area of research? How did you get into this area?

My current area of research is Molecular Epidemiology and Functional Biology of Infectious Pathogens. While H.pylori and Leptospires are pathogens of interest, the major focus is on Mycobacterium tuberculosis the bacterium that causes tuberculosis (TB). In the over 30 years of my research career, I firmly believe that `change is the only constant in life’ and keeping this philosophy in mind, the research focus in my lab has been shifting over time.

After starting my independent research group, following my Post-doctoral training in the US and Canada on baculovirus mediated gene expression in insect cells, I switched over to tuberculosis. The reason for this shift has been the realization that publishing good papers in good journals is one thing, but having your scientific discovery make an impact on human kind is altogether different. I, therefore, deliberately chose tuberculosis because of the devastation the disease causes taking approximately one human life every 15 seconds somewhere in the world. In the background was also the excitement about the sequencing of the total genome of Mycobacterium tuberculosis. We started by dissecting the molecular epidemiology of this pathogen in India, using the powers of DNA profiling, and then moving on to address the question of functional biology with a view to identify new diagnostics and new targets for developing inhibitors for intervention against tuberculosis.

2. You have published several papers in PLoS ONE to date. Can you tell us which one was the best received and, perhaps, why?

I have about half a dozen papers in PLoS ONE so far. The reason for selecting PLoS ONE is the impression that this journal, part of the prestigious PLoS family, transcends disciplines, something which Science and Nature does (unlike other members of the PLoS family which are more subject specific). Our work is of wide interest, therefore publishing in such a journal will attract a wider readership, as opposed to publishing in a specialized journal where specialists would primarily be drawn to your findings.

On the issue of which of my papers was the best received so far, it is hard to say because it is only about a year since we published our first paper. Our latest one has to do with diabetes and tuberculosis, a synergy which is emerging as a major concern across the world and I am sure this will also attract much greater attention.

3. Why did you and your team choose PLoS ONE to publish this work?

We chose PLoS ONE for the simple reason of the wider audience. The time that PLoS ONE takes in taking a final decision is another factor. I try to avoid journals which take months to arrive at a final decision. What I also like in PLoS ONE is the proactive due diligence on accepted papers which PLoS ONE conducts and, based on its judgment, the press releases it issues to create wider awareness outside the normal readership. In addition, their publishing platform which allows scientists to debate your published data on the net is perhaps unique to PLoS and this enables your peers, and also your possible competitors, to address questions and provide critiques.

4. What are you working on now?

My lab continues to work on molecular infection biology of Mycobacterium tuberculosis and also the dissemination dynamics of this bacterium. We have some very exciting stories about some of the unique features the bacteria has for the host immune system and then finally, after the right signals are received from the host, embark on a major effort for its own dissemination and survival. We are also collaborating with other colleagues to sequence the genome of a soil mycobacterium which is of great interest to people working not only in treatment of tuberculosis but also other inflammatory disorders.

5. What was your experience of publishing with us like?

As I said earlier, my experience has been wonderful so far and I am sure I would like to publish more and more in PLoS ONE. The wider readership and the broad canvass on which it operates certainly provokes me to send my manuscripts to PLoS ONE.

Adam Ratner, MD is an Assistant Professor of Pediatrics and Microbiology at Columbia University. He is one of the first people to join the Editorial Board at PLoS ONE and is now our Section Editor for Infectious Diseases. We talked over Skype about medicine, Open Access, PLoS and the world of scientific publishing.

BZ: I’d like to start with a bit more detail on your scientific and medical background – what brought you into infectious diseases research?

My interest and my clinical training are in pediatric infectious diseases. My research direction started during a postdoctoral stint at University of Pennsylvania where I could see the power of new methods: we could simultaneously genetically modify a pathogen – Streptococcus pneumoniae, the bacterium responsible for a number of childhood diseases, and its model host – the mouse. With this approach we could study both how the pathogen affects the host and how the host responds to the pathogen.

Most of my work is now focused on research, but for about eight weeks every year I treat pediatric patients. I find it good to combine the lab and the clinic as the two inform each other.

The following year, when PLoS announced the founding of PLoS ONE, I was intrigued. I admit I was a little skeptical at first, but more I thought about it, more I realized that a journal like this – of broad scope, accepting papers that are scientifically sound without regard to potential impact, is exactly what the scientific community needed. Soon I became a believer, and joined the Academic Board among the very first people to do so, at the beginning of the journal.

BZ: How many hours a week would you say you devote to PLoS ONE and when do you fit that into your busy schedule?

I try to devote 1-2 hours to PLoS ONE every day, as I understand the need for quick turnaround. So I try to move the manuscripts to Academic Editors and reviewers quickly.

BZ: How does the peer-review process on PLoS ONE work? What is the standard of peer-review on PLoS ONE?

In some ways, the review system in PLoS ONE is very similar to other journals in the areas of infectious diseases or microbiology, yet in other ways it is very different. The process is identical to other journals in that manuscripts are sent out to reviewers who do their job seriously and apply the same scientific standards to the work. On the other hand, it makes a huge difference that no manuscript is rejected early because “it is not of interest to us” – there are none of those limitations.

Thus, the reviewing process is rigorous – reviewers are evaluating if the work is hypothesis driven, is the work of high quality, and are conclusions supported by the data, but not trying to meet any subjective criteria.

BZ: How quickly does this process move?

Speed is an important aspect of PLoS ONE. I read each manuscript myself, which takes a day or two, and then decide which other Academic Editors or external reviewers to send it to. There, the review process may last an additional two to three weeks or so, at which point we can make a decision to reject, accept with modifications or accept as is.

BZ: What’s the general quality of submissions like?

It is similar to other quality journals. Sure, some manuscripts are sub-par, and our system allows the Academic Editors to reject such papers quickly, without necessarily burdening the external reviewers with them. But most are very good. What is very good about PLoS ONE is that it is a natural home for studies that are interdisciplinary – thus not fitting neatly into other specialized journals’ criteria of what they like to publish. And such interdisciplinary studies are now becoming very frequent. Also, this is a good place for negative or confirmatory results, which, though they may not be exciting, are very useful, especially in clinical areas of biomedical science. The fact that PLoS ONE does not care about the tyranny of Impact Factor allows it to publish a wealth of medically important studies.

The best thing about PLoS ONE is that it does not impose boundaries between disciplines. †Thus, cross-disciplinary work that does not fit neatly anywhere else (as much as there is a lot of lip-service about the importance of such work), fits perfectly in PLoS ONE.

BZ: And finally, what would you say is the thing about Open Access that most excites you?

There is a social justice aspect to Open Access that I find particularly compelling. Especially, as we just mentioned, in the international sphere: making sure that all the existing medical knowledge is available to physicians everywhere on the planet.

BZ: Thank you very much for your time. It was great fun talking to you.

And for the readers: if you would like to experience PLoS ONE for yourself, submit your work to us today.

Tom Tregenza is a Royal Society Research Fellow at the Centre for Ecology & Conservation at the University of Exeter’s Cornwall campus. He recently became the Section Editor for Evolution at PLoS ONE and in this capacity he has already handled 82 manuscripts. We talked over Skype last week about his science and about the world of scientific publishing.

BZ: I’d like to start with a bit more detail on your scientific background. How did you get into science, and in particular why evolutionary and behavioral biology?

TT: Like many others, I was excited about nature as a child. Living close to the coast here in the UK, where the tides are very large, every time the tide was low it exposed a rich and magical world of creatures living there. Later on, reading Richard Dawkins’ “The Selfish Gene” was a trigger for me to study biology. The elegant concept of Natural Selection is an incredibly powerful explanation for the diversity and adaptations of living creatures. Behavior, in particular, is such a complex emergent property that it is a constant source of wonder. It illustrates the constraints on Natural Selection, where it is really the survival of the fitter, not the fittest, that drives evolution.

I focus my research mainly on sexual selection, where the emphasis is less on the survival of the fittest and more on other ways that genes can increase their representation in the next generation. For instance, my studies on sexual conflict reveal adaptations that favor one member of a mating pair, even if they are bad for his/her (usually his) mate. In a sense, a male is a parasite on the female and mate choice and courtship behaviors are a struggle between the interests of the two.

I started out my postdoctoral studies with Roger Butlin at the University of Leeds, using grasshoppers as a model system. I was interested in their biogeography and what made populations diverge and form new species. Later, I switched to crickets as they are much easier to take care of in the laboratory. After a number of lab studies on crickets in the lab, I am now testing the ideas about sexual conflict and sexual selection in the field. I would like to see if the laboratory results reflect what is really happening out in nature, as well as to develop a model system that can be equally easily studied both indoors and outdoors. We now have 100 cameras trained at the burrows and we are filming marked individuals continuously. We then analyze who mated with whom, genotype the individuals, then genotype their offspring in the next generation.

Finally, I’m involved in an ongoing collaboration with Dr.Mark Norman and Dr.Julian Finn from the museum of Victoria, Melbourne, and the University of Tasmania, studying mimicry in cephalopods. My colleagues go out on the boat, dive, look at the behaviors in the field and make videos. They then send me the video and their ideas and we try to put the work in an evolutionary framework to see what we can learn from cephalopods about nature in general . The observed behaviors are mind-boggling, for example, the mimic octopus can, very quickly, change its shape, posture, color and movements to mimic either a sea snake or a lionfish or some other creatures. We are assuming that there must be something advantageous for the octopus to be able to mimic two or more different predators instead of just one. Perhaps this is frequency-dependent, making it more difficult for predators to learn that the mimic is not actually dangerous. Octopuses are known to be very smart, but this range of dynamic mimicry has not been seen before in any other animal.

TT: It is glaringly obvious that that there are far fewer women at senior levels than at junior levels in science, which does not reflect their abilities. The reasons for this are multifarious, but the resulting gender bias is, first, not fair to the women, and second, not good for science as we are missing their talent. Recent studies suggest that there may be subtle sources of gender disparity in the peer-review system, with manuscripts written by women being judged more strictly than those written by men. Also, as peer-reviewers, men and women behave differently. Biases in peer-review and in academia as a whole are very difficult to study as there are many factors involved. It is not that male scientists are deliberately sexist, but that many aspects of the way science is organized subtly favor men over women. But just because something is difficult to study does not mean we should not study it at all. It is important to make inroads into this study even if the early work is not perfect. Much of the work I’ve done has major limitations, which I do not dispute, however, I think to demand perfection at this early stage of such research is to miss the point of why we are doing it.

BZ: Is this related to what it was that attracted you to PLoS ONE in the first place?

Yes. Peer-review in PLoS ONE gets away from value judgement and subjectivity to a great extent. Work is judged on merit – are the experiments properly done and do conclusions follow from the data. Grading on novelty is a lot of time wasted on debates between editors, reviewers and authors. PLoS ONE got rid of it – the reviewers only judge if the paper is fundamentally sound.

BZ: How many hours a week would you say you devote to PLoS ONE and when do you fit that into your busy schedule?

I’d say I spend about 4 hours per week as a Section Editor at PLoS ONE. And I feel it is time well spent.

BZ: How does the peer-review process on PLoS ONE work?

The peer-review process in PLoS ONE is very similar to many other journals, although I think it has some advantages, especially over the weekly journals, as it concentrates on the question of whether or not the manuscript is fundamentally correct instead of how novel the findings are, which is a subjective judgment. I am actually surprised that we do not see many papers in PLoS ONE that describe repeats or negative results – most of our papers describe novel and original research. Yet, novelty is not what the reviewers are looking at. I would actually like to see more repetitions of famous studies being done and being published.

As a result of the PloS ONE review policy, authors can write more objectively. They do not need to use the polemical marketing tone in order to “sell” their work to the reviewers and editors. In high impact journals, like Science and Nature, manuscripts tend to be ‘sexed-up’ with large claims of novelty, leading to a high rate of Type I errors in such journals. In contrast, peer-review at PLoS ONE is just as rigorous, but authors do not need to apply their salesmanship skills – the research is judged on its own merits.

BZ: What do you feel makes PLoS ONE relevant to scientists? When you suggest to your colleagues to publish in PLoS ONE, what do you tell them?

I tell them that their papers will be widely read and easy to find. The publication is rapid, as the review is not bogged down in discussions about novelty. I also believe that the age of the Impact Factor is shortly going to be behind us and that in the nearest future individual papers will be evaluated regardless of the journal in which they are published.

BZ: Thank you very much for your time. Your research is fascinating and this was a very enjoyable conversation.

If you would like to experience PLoS ONE for yourself, submit your work to us today.

I already wrote one entry for PLoS ONE’s second birthday, but I’m feeling sparky today, and I think I like this paper better.

I don’t know about you guys, but when I was a sprog, my parents dragged me to music lessons. LOTS of music lessons. As of right now, I have been producing music of some type for the past 21 years straight. And I LOVE it.

Of course, I didn’t always love it. I remember my mother dragging me and my brother to lessons, making us sit down every day and practice (I was, and still am, no good with the practicing), and the fear and shakiness of recitals (heck, I still get that, and it’s been 21 years). In her time, Sci has actually “mastered” (it’s a debatable point), three different instruments (‘instruments’ is a loose term), and still uses one of them professionally on occasion. And if you can guess what they are, Sci will…do something cool. Like send you one of her favorite books. Or perhaps a tshirt with a molecule on it. Or perhaps some of her delicious cookies. Obviously, you can only guess if you don’t KNOW already (that means you, Dad). So there you go, contest open.

Anyway, years and years of music lessons. But the question is: did they do me any good? Does playing ‘Baby Mozart’ really do anything, and is anything achieved by starting your child on Suzuki when they are 2, other than the pain and misery of your child, and possibly an eventual love of music? Can it, perhaps, make me SMARTER?

And for the record, Einstein did play the violin. Apparently he was quite good.

There actually are several studies out there that show that techniques that you learn can “transfer” to other techniques, giving you a bit of an edge. This works best when you’re performing skills that are very similar to each other (like learning how to estimate the area of a square, and then learning how to estimate the area of a triangle). We know this happens for musicians in the development of fine motor skills. Once you’ve been playing the violin for a while, other things that require fine motor skills will come to you a bit easier (perhaps we should train all would-be surgeons on musical instruments, if you can master playing Rachmaninoff, brain surgery should be a piece of cake).

Of course, most of the studies that have been done are correlational in nature. Kids who play musical instruments have better motor skills. This could be due to the music, or the kids could play music because they have good motor skills. Good motor skills could be a development of things like the higher socio-economic class that often goes along with being taught music as a child, and thus parents are maybe able to put more effort to their development. The possibilities go on. Correlation is NOT causation.

The same thing goes for the correlation between musical learning and IQ. There was a modest correlation, but it could be just the effect of the extra lessons the kids were receiving, resulting in more time spent on focused attention and mastering a skill. Significant correlations have also been shown for music and verbal and language skills. Music lessons have been found to be correlated with increases in reading ability and phonetic comprehension. This actually leads me to a question: if language, reading, and phonetic comprehension are related to the pitch and tone of words, do children who are tone deaf have a harder time mastering reading and verbal skills? I think this might warrant a future PubMed search.

Unfortunately, all the previous tests tended to focus on the “transfer” of skills to not very related fields, like IQ. So in this study, the authors wanted to look at the effects of music learning on “near” transfers, skill closely related to music training: spatial reasoning, verbal abilities, nonverbal, and mathematical. They also looked for VERY closely related skills: fine motor control and auditory skill.

They grabbed a whole bunch of kids around 8-11 years old. Some played musical instruments, some didn’t (one of the problems with this study to me is that the control group is a good bit small than the instrumental group, 41 musicians vs 18 non). Kids were controlled for the socio-economic class of the parents. Average length of music training was close to five years. They also divided the kids up by whether or not they got Suzuki training, but ended up grouping them together, as Suzuki effects were no different from other instrumentalists.

Dang, they didn’t graph their data. Well, I shall fix. Because I can. People should be so grateful I do all their graphing…

There you go. So, as you can see from the graph (the pretty, pretty graph), musical kids scored a lot better on fine motor skills for left and right hand (the first two sets of bars). This is pretty expected, if you’re using fine motor skills a lot, presumably you’ll get better at them. The musical kids also did better when distinguishing tones and following melody lines, though interestingly, they didn’t show any improvements in rhythm. I wonder if this has anything to do with the kids of music the kids were studying. There wasn’t a single drummer in the bunch, it was all either piano or stringed instruments.

And finally, the kids with musical training scored a lot better (I know it doesn’t look like it, but the MANCOVA analysis uncovered a difference) on vocabulary testing. They outperformed their non-musical counterparts in both verbal ability (vocabulary) and non-verbal reasoning skills. They didn’t find any differences in math or spatial reasoning.

The authors hypothesize that music training may transfer skills to some other related domains. The other hypothesis is that music training doesn’t enhance a specific skill set, but rather your general intellectual ability. This would mean they would score higher on every test given. In fact, they DID score higher, but most of the time the scores didn’t reach significance.

Still, remember this is correlation, not causation. Families were of similar socio-ecoomic class and education, but that doesn’t mean they are all similar parents. Kids who take music lessons may have parents that are more involved in their intellectual development. Kids that persist in taking music lessons for a good chunk of time may have superior motivation. Correlation =/= causation.

But it’s still a cool paper, and no matter what, it’s quite clear that music lessons didn’t HURT. Time to tape your poor child to the piano bench!

“Along food chains, i.e., at different trophic levels, the most abundant taxa often represent exceptional food reservoirs, and are hence the main target of consumers and predators. The capacity of an individual consumer to opportunistically switch towards an abundant food source, for instance, a prey that suddenly becomes available in its environment, may offer such strong selective advantages that ecological innovations may appear and spread rapidly. New predator-prey relationships are likely to evolve even faster when a diet switch involves the exploitation of an unsaturated resource for which few or no other species compete. Using stable isotopes of carbon and nitrogen as dietary tracers, we provide here strong support to the controversial hypothesis that the giant noctule bat Nyctalus lasiopterus feeds on the wing upon the multitude of flying passerines during their nocturnal migratory journeys, a resource which, while showing a predictable distribution in space and time, is only seasonally available. So far, no predator had been reported to exploit this extraordinarily diverse and abundant food reservoir represented by nocturnally migrating passerines.”

“In discussions of Open Access, we always focus on brand new papers and how to make them freely available for readers around the world as well as for people who want to mine and reanalyse the data using robots. But we almost never discuss the need to make the old stuff available. Yet we often lament that nobody reads or cites anything older than five years. Spending several years reading everything published in the field in the 20th century up until about 1995 (as well as some 19th century stuff) helped me greatly in my own research. It would help others, I’m sure, especially those who are now revisiting old questions with new techniques. How are the classical papers going to be made available for today’s students?

SRBR is working on it now, and I assume that this will be done piece-meal, with each society doing their own work on making old literature available. What I saw (not yet available for public) is a development of a ChronoHistory website. Yes, people will send in pictures and anecdotes and old posters and stuff (and I hope once that material is online that SRBR will get a professional historian of science to make sense of it all), but the most important part of the site will be a repository of the old papers. Services of a real science librarian have been secured to deal with everything from copyright to technical problems in order to provide copies of many old papers on the site. Probably some of the papers will be available to everyone for free while others, due to copyright, may be available only to SRBR members with a password.”

Peter says: “Ultimately we need all peer-reviewed journals to digitize their backfiles for OA. Some are already doing it. Some are digitizing their backfiles but charging for access. Some can’t afford to digitize their backfiles at all.”

Google is willing to digitize the backfile of any journal. Peter blogged about it in December 2006, although Google still doesn’t have a web page for the program. The Google deal isn’t very good. But for journals that can’t find any other funds to digitize their backfile, Peter thinks it’s better than nothing. Google does not have a website for this, but see this interview (this August 2007 interview – via):

Representing another effort to reach currently inaccessible content, Google Scholar now has its own digitization program. “It’s a small program,” said Acharya. “We mainly look for journals that would otherwise never get digitized. Under our proposal, we will digitize and host journal articles with the provision that they must be openly reachable in collaboration with publishers, fully downloadable, and fully readable. Once you get out of the U.S. and Western European space into the rest of the world, the opportunities to get and digitize research are very limited. They are often grateful for the help. It gives us the opportunity to get that country’s material or make that scholarly society more visible.”

Peter also said (personal communication): “As far as I know, the Open Content Alliance doesn’t (yet) digitize journals, but I hope it will start. However, when Google digitizes print literature it pays all the costs (and slightly restricts use of the results); but when OCA digitizes print lit, it requires the possessor or a donor to pay the costs (and provides full OA to the results).”

What do you all think? What is your Society doing about this, you favourite Journals?

Open Students is a new blog for students about open access to research. It is run by Gavin Baker (who also recently joined Peter Suber at Open Access News – Congratulations!) and sponsored by SPARC, the Scholarly Publishing and Academic Resources Coalition, as part of its student outreach activities.

The blog will cover the issues of Open Science as it affects the college students and will have frequent guest-bloggers (students, librarians, researchers, publishers…) – of which you can be one if you contact Gavin.

Scienceblogging.org

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